6LI0

Crystal structure of GPR52 in complex with agonist c17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of ligand recognition and self-activation of orphan GPR52.

Lin, X.Li, M.Wang, N.Wu, Y.Luo, Z.Guo, S.Han, G.W.Li, S.Yue, Y.Wei, X.Xie, X.Chen, Y.Zhao, S.Wu, J.Lei, M.Xu, F.

(2020) Nature 579: 152-157

  • DOI: 10.1038/s41586-020-2019-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • GPR52 is a class-A orphan G-protein-coupled receptor that is highly expressed in the brain and represents a promising therapeutic target for the treatment of Huntington's disease and several psychiatric disorders <sup>1,2 </sup>. Pathological malfunc ...

    GPR52 is a class-A orphan G-protein-coupled receptor that is highly expressed in the brain and represents a promising therapeutic target for the treatment of Huntington's disease and several psychiatric disorders 1,2 . Pathological malfunction of GPR52 signalling occurs primarily through the heterotrimeric G s protein 2 , but it is unclear how GPR52 and G s couple for signal transduction and whether a native ligand or other activating input is required. Here we present the high-resolution structures of human GPR52 in three states: a ligand-free state, a G s -coupled self-activation state and a potential allosteric ligand-bound state. Together, our structures reveal that extracellular loop 2 occupies the orthosteric binding pocket and operates as a built-in agonist, conferring an intrinsically high level of basal activity to GPR52 3 . A fully active state is achieved when G s is coupled to GPR52 in the absence of an external agonist. The receptor also features a side pocket for ligand binding. These insights into the structure and function of GPR52 could improve our understanding of other self-activated GPCRs, enable the identification of endogenous and tool ligands, and guide drug discovery efforts that target GPR52.


    Organizational Affiliation

    Shanghai Institute of Precision Medicine, Shanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, USA.,University of Chinese Academy of Sciences, Beijing, China.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. leim@shsmu.edu.cn.,Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China.,Shanghai Institute of Precision Medicine, Shanghai, China. leim@shsmu.edu.cn.,iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Precision Medicine, Shanghai, China. wujian@shsmu.edu.cn.,Centre for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China. xufei@shanghaitech.edu.cn.,iHuman Institute, ShanghaiTech University, Shanghai, China. xufei@shanghaitech.edu.cn.,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China. wujian@shsmu.edu.cn.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. wujian@shsmu.edu.cn.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China. xufei@shanghaitech.edu.cn.,CAS Key Laboratory of Receptor Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Cell Differentiation and Apoptosis, Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China. leim@shsmu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chimera of G-protein coupled receptor 52 and Flavodoxin
A
468Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Homo sapiens
This entity is chimeric
Mutation(s): 8 
Gene Names: GPR52
Find proteins for P00323 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P00323
Find proteins for Q9Y2T5 (Homo sapiens)
Go to Gene View: GPR52
Go to UniProtKB:  Q9Y2T5
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
EN6
Query on EN6

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Download CCD File 
A
N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoromethyl)phenyl]methyl]-1-benzothiophen-7-yl]pyrazole-4-carboxamide
C24 H22 F3 N3 O3 S
VJMRKWPMFQGIPI-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

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Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

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Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.970α = 90.00
b = 88.360β = 90.00
c = 156.280γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History 

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2020-03-04
    Type: Database references
  • Version 1.2: 2020-03-18
    Type: Database references